Limosilactobacillus fermentum in the theoretical composition was changed to Lactobacillus fermentum
## Error in validObject(.Object) : invalid class "otu_table" object:
## OTU abundance data must have non-zero dimensions.
These are the taxa that were found in the experimental data
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.0964 0.01882 0.2301 0.367
## Residual 24 5.0274 0.98118
## Total 26 5.1238 1.00000
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.136 0.0252 0.3102 0.175
## Residual 24 5.261 0.9748
## Total 26 5.397 1.0000
### PERMANOVA
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.1361 0.02519 0.3101 0.204
## Residual 24 5.2675 0.97481
## Total 26 5.4036 1.00000
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.1690 0.02807 0.3466 0.075 .
## Residual 24 5.8511 0.97193
## Total 26 6.0202 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms", strata = sampdat$source)
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.1383 0.02149 0.2635 0.163
## Residual 24 6.2977 0.97851
## Total 26 6.4360 1.00000